If the MAF was broken it would likely throw a code although not always.
With the whistle noise you mention, without hearing it in person, my thoughts go to a boost/vac leak which does not always trigger an engine light or code but could cause poor running conditions. Does it do it all the time and without engine load (IE not driving anywhere and gearbox in neutral?) The supercharger turns itself on and off throughout a drive and thus you switch between running vacuum and boosted air pressure. With the gearbox in neutral and from idle, bring the revs up to around 2000rpm and you should hear the supercharger initially and after a short while, it will turn off - does the whistle noise change?
Are you able to video record it and place it online, such as youtube? Are you able to pin point or identify its rough location within the engine bay?
Does your diagnostic tool allow you to read the long term and short term fuel trim values from the ECU at all? These values show you that the engine is attempting to compensate the factory fuel map due to an issue, such as an air leak. If I remember correctly 0 or very low values are to be expected (IE between -10 and +10), however high values (in both positive and negative) may indicate an issue.
Did you remove and tweak any pipes at all when you were working on the car or accidently slip? Maybe you forgot to pop one back on, one has split or come off if not seated correctly so worth double checking.
Have you checked the airbox is seated correctly after replacing the air filter? I find the airbox difficult to deal with and could be miss-aligned/gap. When this happens however you wont be getting the security clips hooked over. However this is unlikely to cause any of your poor performance issues but could generate noise when the supercharger runs as the airbox also acts as an intake silencer - the supercharger whine without the airbox seated properly (or at all) is surprisingly loud!
